The Genetics of Heterostyly

Genomic analyses elucidate S-locus evolution in response to intra-specific losses of distyly in Primula vulgaris

Distyly, a floral dimorphism that promotes outcrossing, is controlled by a hemizygous genomic region known as the S-locus. Disruptions of genes within the S-locus are responsible for the loss of distyly and the emergence of homostyly, a floral monomorphism that favors selfing. Using whole-genome resequencing data of distylous and homostylous individuals from populations of Primula vulgaris and leveraging high-quality reference genomes of Primula we tested, for the first time, predictions about the evolutionary consequences of transitions to selfing on S-genes. Our results reveal a previously undetected structural rearrangement in CYPᵀ associated with the shift to homostyly and confirm previously reported, homostyle-specific, loss-of-function mutations in the exons of the S-gene CYPᵀ. We also discovered that the promoter and intronic regions of CYPᵀ in distylous and homostylous individuals are conserved, suggesting that down-regulation of CYPᵀ via mutations in its promoter and intronic regions is not a cause of the shift to homostyly. Furthermore, we found that hemizygosity is associated with reduced genetic diversity in S-genes compared with their paralogs outside the S-locus. Additionally, the shift to homostyly lowers genetic diversity in both the S-genes and their paralogs, as expected in primarily selfing plants. Finally, we tested, for the first time, long-standing theoretical models of changes in S-locus genotypes during early stages of the transition to homostyly, supporting the assumption that two copies of the S-locus might reduce homostyle fitness.

Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica

Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.

The yield of common buckwheat (Fagopyrum esculentum Moench) depends on the genotype but not on the Pin-to-Thrum ratio

Common buckwheat has a complicated flowering biology. It is characterized by a strong self-incompatibility resulting from heterostyly, i.e. the occurrence of two types of flowers: Pin and Thrum, differing in the length of pistils and stamens. Fertilization occurs only as a result of cross-pollination between these morphs. Suspicions exist that the disturbed ratio between plants producing Pin and Thrum flowers (with the latter type generating more seeds) causes low seed yield. The aim of the study was to analyze: (1) the ratio between plants with Pin and Thrum morphs, (2) flower and seed production, as well as abortion of flowers, (3) the composition of nectar collected at an early flowering stage and during full flowering. The study was performed under semi-controlled and field conditions on six Polish accessions. The results indicated that under semi-controlled conditions the Pin-to-Thrum ratio was indeed disproportionate; such a phenomenon is called anisoplethy. In the field, however, the Pin-to-Thrum ratio was well-balanced (isoplethy). The plants with both morphs aborted a similar percentage of flowers and produced a comparable number of empty seeds. The number of flowers, their abortion, and ripe seed production were independent of flower type, however, they were genotypically controlled. A strong correlation between the number of flowers produced by a plant, flower abortion and the number of empty seeds was found. The percentage of aborted flowers correlated positively with the weight of ripe seeds. Nectar composition was similar for all buckwheat genotypes, but we found some differences in the amount of individual sugars depending on the blooming stage. In the majority of accessions, the nectar produced at the early blooming stage was characterized by a greater mass and volume, and contained more individual sugars than at the full-flowering stage.

Two floral forms in the same species-distyly

MAIN CONCLUSION

This paper reviews the progress of research on the morphology, physiology and molecular biology of distyly in plants. It will help to elucidate the mysteries of distyly in plants. Distyly is a unique representative type of heterostyly in plants, primarily characterized by the presence of long style and short style within the flowers of the same species. This interesting trait has always fascinated researchers. With the rapid development of molecular biology, the molecular mechanism for the production of dimorphic styles in plants is also gaining ground. Researchers have been studying plant dimorphic styles from various perspectives. The researchers are gradually unravelling the mechanisms by which plants produce distyly traits. This paper reviews advances in the study of plant dimorphic style characteristics, mainly in terms of the morphology, physiology and molecular biology of plants with dimorphic styles. The aim is to provide a theoretical basis for the study of the mechanism of distyly formation in plants.

Inheritance of distyly and homostyly in self-incompatible Primula forbesii

The evolutionary transition from self-incompatible distyly to self-compatible homostyly frequently occurs in heterostylous taxa. Although the inheritance of distyly and homostyly has been deeply studied, our understanding on modifications of the classical simple Mendelian model is still lacking. Primula forbesii, a biennial herb native to southwest China, is a typical distylous species, but after about 20 years of cultivation with open pollination, self-compatible homostyly appeared, providing ideal material for the study of the inheritance of distyly and homostyly. In this study, exogenous homobrassinolide was used to break the heteromorphic incompatibility of P. forbesii. Furthermore, we performed artificial pollination and open-pollination experiments to observe the distribution of floral morphs in progeny produced by different crosses. The viability of seeds from self-pollination was always the lowest among all crosses, and the homozygous S-morph plants (S/S) occurred in artificial pollination experiments but may experience viability selection. The distyly of P. forbesii is governed by a single S-locus, with S-morph dominant hemizygotes (S/-) and L-morph recessive homozygotes (-/-). Homostylous plants have a genotype similar to L-morph plants, and homostyly may be caused by one or more unlinked modifier genes outside the S-locus. Open pollinations confirm that autonomous self-pollination occurs frequently in L-morphs and homostylous plants. This study deepens the understanding of the inheritance of distyly and details a case of homostyly that likely originated from one or more modifier genes.

Comprehensive transcriptomic profiling reveals complex molecular mechanisms in the regulation of style-length dimorphism in Guettarda speciosa (Rubiaceae), a species with "anomalous" distyly

BACKGROUND

The evolution of heterostyly, a genetically controlled floral polymorphism, has been a hotspot of research since the 19th century. In recent years, studies on the molecular mechanism of distyly (the most common form of heterostyly) revealed an evolutionary convergence in genes for brassinosteroids (BR) degradation in different angiosperm groups. This floral polymorphism often exhibits considerable variability that some taxa have significant stylar dimorphism, but anther height differs less. This phenomenon has been termed "anomalous" distyly, which is usually regarded as a transitional stage in evolution. Compared to "typical" distyly, the genetic regulation of "anomalous" distyly is almost unknown, leaving a big gap in our understanding of this special floral adaptation strategy.

METHODS

Here we performed the first molecular-level study focusing on this floral polymorphism in Guettarda speciosa (Rubiaceae), a tropical tree with "anomalous" distyly. Comprehensive transcriptomic profiling was conducted to examine which genes and metabolic pathways were involved in the genetic control of style dimorphism and if they exhibit similar convergence with "typical" distylous species.

RESULTS

"Brassinosteroid homeostasis" and "plant hormone signal transduction" was the most significantly enriched GO term and KEGG pathway in the comparisons between L- and S-morph styles, respectively. Interestingly, homologs of all the reported S-locus genes either showed very similar expressions between L- and S-morph styles or no hits were found in G. speciosa. BKI1, a negative regulator of brassinosteroid signaling directly repressing BRI1 signal transduction, was identified as a potential gene regulating style length, which significantly up-regulated in the styles of S-morph.

DISCUSSION

These findings supported the hypothesis that style length in G. speciosa was regulated through a BR-related signaling network in which BKI1 may be one key gene. Our data suggested, in species with "anomalous" distyly, style length was regulated by gene differential expressions, instead of the "hemizygous" S-locus genes in "typical" distylous flowers such as Primula and Gelsemium, representing an "intermediate" stage in the evolution of distyly. Genome-level analysis and functional studies in more species with "typical" and "anomalous" distyly would further decipher this "most complex marriage arrangement" in angiosperms and improve our knowledge of floral evolution.

Genomic evidence supports the genetic convergence of a supergene controlling the distylous floral syndrome

Heterostyly, a plant sexual polymorphism controlled by the S-locus supergene, has evolved numerous times among angiosperm lineages and represents a classic example of convergent evolution in form and function. Determining whether underlying molecular convergence occurs could provide insights on constraints to floral evolution. Here, we investigated S-locus genes in distylous Gelsemium (Gelsemiaceae) to determine whether there is evidence of molecular convergence with unrelated distylous species. We used several approaches, including anatomical measurements of sex-organ development and transcriptome and whole-genome sequencing, to identify components of the S-locus supergene. We also performed evolutionary analysis with candidate S-locus genes and compared them with those reported in Primula and Turnera. The candidate S-locus supergene of Gelsemium contained four genes, of which three appear to have originated from gene duplication events within Gelsemiaceae. The style-length genes GeCYP in Gelsemium and CYP734A50 in Primula likely arose from duplication of the same gene, CYP734A1. Three out of four S-locus genes in Gelsemium elegans were hemizygous, as previously reported in Primula and Turnera. We provide genomic evidence on the genetic convergence of the supergene underlying distyly among distantly related angiosperm lineages and help to illuminate the genetic architecture involved in the evolution of heterostyly.

Different molecular changes underlie the same phenotypic transition: Origins and consequences of independent shifts to homostyly within species

The repeated transition from outcrossing to selfing is a key topic in evolutionary biology. However, the molecular basis of such shifts has been rarely examined due to lack of knowledge of the genes controlling these transitions. A classic example of mating system transition is the repeated shift from heterostyly to homostyly. Occurring in 28 angiosperm families, heterostyly is characterized by the reciprocal position of male and female sexual organs in two (or three) distinct, usually self-incompatible floral morphs. Conversely, homostyly is characterized by a single, self-compatible floral morph with reduced separation of male and female organs, facilitating selfing. Here, we investigate the origins of homostyly in Primula vulgaris and its microevolutionary consequences by integrating surveys of the frequency of homostyles in natural populations, DNA sequence analyses of the gene controlling the position of female sexual organs (CYPᵀ), and microsatellite genotyping of both progeny arrays and natural populations characterized by varying frequencies of homostyles. As expected, we found that homostyles displace short-styled individuals, but long-style morphs are maintained at low frequencies within populations. We also demonstrated that homostyles repeatedly evolved from short-styled individuals in association with different types of loss-of-function mutations in CYPᵀ. Additionally, homostyly triggers a shift to selfing, promoting increased inbreeding within and genetic differentiation among populations. Our results elucidate the causes and consequences of repeated transitions to homostyly within species, and the putative mechanisms precluding its fixation in P. vulgaris. This study represents a benchmark for future analyses of losses of heterostyly in other angiosperms.

The rapid appearance of homostyly in a cultivated distylous population of Primula forbesii

Evolutionary breakdown from rigorous outbreeding to self-fertilization frequently occurs in angiosperms. Since the pollinators are not necessary, self-compatible populations often reduce investment in floral display characteristics and pollination reward. Primula forbesii is a biennial herb with distribution restricted to southwest China; it was initially a self-incompatible distylous species, but after 20 years of artificial domestication, homostyly appeared. This change in style provides an ideal material to explore the time required for plant mating systems to adapt to new environmental changes and test whether flower attraction has reduced following transitions to selfing. We did a survey in wild populations of P. forbesii where its seeds were originally collected 20 years ago and recorded the floral morph frequencies and morphologies. The floral morphologies, self-incompatibility, floral scent, and pollinator visitation between distyly and homostyly were compared in greenhouse. Floral morph frequencies of wild populations did not change, while the cultivated population was inclined to L-morph and produced homostyly. Evidence from stigma papillae and pollen size supports the hypothesis that the homostyly possibly originated from mutations of large effect genes in distylous linkage region. Transitions to self-compatible homostyly are accompanied by smaller corolla size, lower amounts of terpenoids, especially linalool and higher amounts of fatty acid derivatives. The main pollinators in the greenhouse were short-tongued Apis cerana. However, homostyly had reduced visiting frequency. The mating system of P. forbesii changed rapidly in just about 20 years of domestication, and our findings confirm the hypothesis that the transition to selfing is accompanied by decreased flower attraction.

Variation in pollen sterility and gender specialization: an investigation with distylous species of Erythroxylum (Erythroxylaceae)

Differences in pollen sterility between morphs in distylous populations may represent the first step in the evolution of gender specialization. Theoretically, for partially or completely male sterile individuals to persist they must have some fitness advantage that compensates for the loss of male function. Gender specialization is considered a widespread process in Erythroxylum, but male sterility and the resource reallocation to female function have been investigated in few species and populations. In 18 populations of four distylous species of Erythroxylum, we quantified the levels of male sterility, estimated through pollen sterility, in short- and long-styled flowers to test if sterility is morph-biased. In one population per species, we also described the frequency of floral visitors, the production of flowers and fruits, and the quality of fruits and seeds of short- and long-styled plants to evaluate the expression of trade-offs in allocation to male and female function. In some populations of E. campestre and E. deciduum, short-styled flowers possessed higher levels of pollen sterility than long-styled flowers. Although most flowers of E. suberosum and E. tortuosum also expressed pollen sterility, the frequency of sterility was similar between morphs in all populations. Differences in reproductive output between morphs occurred only in populations of species with morph-biased sterility, but none of the variations reflect resource allocation to female fitness of short-styled plants. Differences in the level of sterility between morphs indicates the potential for gender specialization in populations of E. campestre and E. deciduum, despite the apparent lack of a trade-off in allocation.

Pistil Mating Type and Morphology Are Mediated by the Brassinosteroid Inactivating Activity of the S-Locus Gene BAHD in Heterostylous Turnera Species

Heterostyly is a breeding system that promotes outbreeding through a combination of morphological and physiological floral traits. In Turnera these traits are governed by a single, hemizygous S-locus containing just three genes. We report that the S-locus gene, BAHD, is mutated and encodes a severely truncated protein in a self-compatible long homostyle species. Further, a self-compatible long homostyle mutant possesses a T. krapovickasii BAHD allele with a point mutation in a highly conserved domain of BAHD acyl transferases. Wild type and mutant TkBAHD alleles were expressed in Arabidopsis to assay for brassinosteroid (BR) inactivating activity. The wild type but not mutant allele caused dwarfism, consistent with the wild type possessing, but the mutant allele having lost, BR inactivating activity. To investigate whether BRs act directly in self-incompatibility, BRs were added to in vitro pollen cultures of the two mating types. A small morph specific stimulatory effect on pollen tube growth was found with 5 µM brassinolide, but no genotype specific inhibition was observed. These results suggest that BAHD acts pleiotropically to mediate pistil length and physiological mating type through BR inactivation, and that in regard to self-incompatibility, BR acts by differentially regulating gene expression in pistils, rather than directly on pollen.

Biotechnological Methods for Buckwheat Breeding

The Fagopyrum genus includes two cultivated species, namely common buckwheat (F. esculentum Moench) and Tartary buckwheat (F. tataricum Gaertn.), and more than 25 wild buckwheat species. The goal of breeders is to improve the properties of cultivated buckwheat with methods of classical breeding, with the support of biotechnological methods or a combination of both. In this paper, we reviewed the possibility to use transcriptomics, genomics, interspecific hybridization, tissue cultures and plant regeneration, molecular markers, genetic transformation, and genome editing to aid in both the breeding of buckwheat and in the identification and production of metabolites important for preserving human health. The key problems in buckwheat breeding are the unknown mode of inheritance of most traits, associated with crop yield and the synthesis of medicinal compounds, low seed yield, shedding of seeds, differential flowering and seed set on branches, and unknown action of genes responsible for the synthesis of buckwheat metabolites of pharmaceutical and medicinal interest.

Do s genes or deleterious recessives control late-acting self-incompatibility in Handroanthus heptaphyllus (Bignoniaceae)? A diallel study with four full-sib progeny arrays

BACKGROUND AND AIMS

Genetically controlled self-incompatibility (SI) mechanisms constrain selfing and thus have contributed to the evolutionary diversity of flowering plants. In homomorphic gametophytic SI (GSI) and homomorphic sporophytic SI (SSI), genetic control is usually by the single multi-allelic locus S. Both GSI and SSI prevent self pollen tubes reaching the ovary and so are pre-zygotic in action. In contrast, in taxa with late-acting self-incompatibility (LSI), rejection is often post-zygotic, since self pollen tubes grow to the ovary, where fertilization may occur prior to floral abscission. Alternatively, lack of self fruit set could be due to early-acting inbreeding depression (EID). The aim of our study was to investigate mechanisms underlying the lack of selfed fruit set in Handroanthus heptaphyllus in order to assess the likelihood of LSI versus EID.

METHODS

We employed four full-sib diallels to study the genetic control of LSI in H. heptaphyllus using a precociously flowering variant. We also used fluorescence microscopy to study the incidence of ovule penetration by pollen tubes in pistils that abscised following pollination or initiated fruits.

KEY RESULTS

All diallels showed reciprocally cross-incompatible full sibs (RCIs), reciprocally cross-compatible full sibs (RCCs) and non-reciprocally compatible full sibs (NRCs) in almost equal proportions. There was no significant difference between the incidences of ovule penetrations in abscised pistils following self- and cross-incompatible pollinations, but those in successful cross-pollinations were around 2-fold greater.

CONCLUSIONS

A genetic model postulating a single S locus with four S alleles, one of which, in the maternal parent, is dominant to the other three, will produce RCI, RCC and NRC full sib situations each at 33 %, consistent with our diallel results. We favour this simple genetic control over an EID explanation since none of our pollinations, successful or unsuccessful, resulted in partial embryo development, as would be expected under a whole-genome EID effect.

The Genomic Architecture and Evolutionary Fates of Supergenes

Supergenes are genomic regions containing sets of tightly linked loci that control multi-trait phenotypic polymorphisms under balancing selection. Recent advances in genomics have uncovered significant variation in both the genomic architecture as well as the mode of origin of supergenes across diverse organismal systems. Although the role of genomic architecture for the origin of supergenes has been much discussed, differences in the genomic architecture also subsequently affect the evolutionary trajectory of supergenes and the rate of degeneration of supergene haplotypes. In this review, we synthesize recent genomic work and historical models of supergene evolution, highlighting how the genomic architecture of supergenes affects their evolutionary fate. We discuss how recent findings on classic supergenes involved in governing ant colony social form, mimicry in butterflies, and heterostyly in flowering plants relate to theoretical expectations. Furthermore, we use forward simulations to demonstrate that differences in genomic architecture affect the degeneration of supergenes. Finally, we discuss implications of the evolution of supergene haplotypes for the long-term fate of balanced polymorphisms governed by supergenes.

The Turnera Style S-Locus Gene TsBAHD Possesses Brassinosteroid-Inactivating Activity When Expressed in Arabidopsis thaliana

Heterostyly distinct hermaphroditic floral morphs enforce outbreeding. Morphs differ structurally, promote cross-pollination, and physiologically block self-fertilization. In Turnera the self-incompatibility (S)-locus controlling heterostyly possesses three genes specific to short-styled morph genomes. Only one gene, TsBAHD, is expressed in pistils and this has been hypothesized to possess brassinosteroid (BR)-inactivating activity. We tested this hypothesis using heterologous expression in Arabidopsis thaliana as a bioassay, thereby assessing growth phenotype, and the impacts on the expression of endogenous genes involved in BR homeostasis and seedling photomorphogenesis. Transgenic A. thaliana expressing TsBAHD displayed phenotypes typical of BR-deficient mutants, with phenotype severity dependent on TsBAHD expression level. BAS1, which encodes an enzyme involved in BR inactivation, was downregulated in TsBAHD-expressing lines. CPD and DWF, which encode enzymes involved in BR biosynthesis, were upregulated. Hypocotyl growth of TsBAHD dwarfs responded to application of brassinolide in light and dark in a manner typical of plants over-expressing genes encoding BR-inactivating activity. These results provide empirical support for the hypothesis that TsBAHD possesses BR-inactivating activity. Further this suggests that style length in Turnera is controlled by the same mechanism (BR inactivation) as that reported for Primula, but using a different class of enzyme. This reveals interesting convergent evolution in a biochemical mechanism to regulate floral form in heterostyly.

Supergene evolution via stepwise duplications and neofunctionalization of a floral-organ identity gene

Heterostyly represents a fascinating adaptation to promote outbreeding in plants that evolved multiple times independently. While l-morph individuals form flowers with long styles, short anthers, and small pollen grains, S-morph individuals have flowers with short styles, long anthers, and large pollen grains. The difference between the morphs is controlled by an S-locus "supergene" consisting of several distinct genes that determine different traits of the syndrome and are held together, because recombination between them is suppressed. In Primula, the S locus is a roughly 300-kb hemizygous region containing five predicted genes. However, with one exception, their roles remain unclear, as does the evolutionary buildup of the S locus. Here we demonstrate that the MADS-box GLOBOSA2 (GLO2) gene at the S locus determines anther position. In Primula forbesii S-morph plants, GLO2 promotes growth by cell expansion in the fused tube of petals and stamen filaments beneath the anther insertion point; by contrast, neither pollen size nor male incompatibility is affected by GLO2 activity. The paralogue GLO1, from which GLO2 arose by duplication, has maintained the ancestral B-class function in specifying petal and stamen identity, indicating that GLO2 underwent neofunctionalization, likely at the level of the encoded protein. Genetic mapping and phylogenetic analysis indicate that the duplications giving rise to the style-length-determining gene CYP734A50 and to GLO2 occurred sequentially, with the CYP734A50 duplication likely the first. Together these results provide the most detailed insight into the assembly of a plant supergene yet and have important implications for the evolution of heterostyly.

Development of co-dominant markers linked to a hemizygous region that is related to the self-compatibility locus (S) in buckwheat (Fagopyrum esculentum)

Common buckwheat (Fagopyrum esculentum) is a heterostylous self-incompatible (SI) species with two different flower morphologies, pin and thrum. The SI trait is controlled by a single gene complex locus, S. Self-compatible (SC) lines were developed by crossing F. esculentum and F. homotropicum; these lines have an SC gene, Sh , which is dominant over the s allele and recessive to the S allele. S-ELF3 has been identified as a candidate gene in the S locus and is present in the S and Sh but not s alleles. A single-nucleotide deletion in the S-ELF3 gene of the Sh allele results in a frame shift. To develop co-dominant markers to distinguish between ShSh and Shs plants, we performed a next-generation sequencing analysis in combination with bulked-segregant analysis. We developed four co-dominant markers linked to the S locus. We investigated the polymorphism frequency between a self-compatible line and leading Japanese buckwheat cultivars. Linkage between a developed sequence-tagged-site marker and flower morphology was confirmed using more than 1000 segregating plants and showed no recombination. The developed markers would be useful for buckwheat breeding and also to produce lines for genetic analysis such as recombinant inbred lines.

Current status and prospects of common buckwheat breeding in Japan

In this review, the current status and prospects of common buckwheat (Fagopyrum esculentum Moench.) breeding in Japan are summarized. The varieties that have been registered in Japan so far are introduced with details regarding their breeding source populations and breeding methods. Because the main breeding method used for common buckwheat is mass selection, the merits and demerits of this method are explored from the perspective of heritability. Although there are many breeding objectives in common buckwheat, high yield and yield stability are discussed here. Regarding the potential of common buckwheat breeding in the future, the prospects of effective exploitation of self-fertility and selection based on genomic information are examined.

Buckwheat heteromorphic self-incompatibility: genetics, genomics and application to breeding

Common buckwheat (Fagopyrum esculentum Moench 2n = 2x = 16) is an outcrossing crop with heteromorphic self-incompatibility due to its distylous flowers, called pin and thrum. In pin plants, a long style is combined with short stamens and small pollen grains; in thrum plants, a short style is combined with long stamens and large pollen grains. Both the intra-morph self-incompatibility and flower morphology are controlled by a single genetic locus named the S locus; thrum plants are heterozygous (Ss) and pin plants are homozygous recessive (ss) at this locus. Self-incompatibility is an obstacle for establishing pure lines and fixation of agronomically useful genes. Elucidation of the molecular mechanism of heterostylous self-incompatibility of common buckwheat has continued for a quarter of a century. Recent advances in genomic and transcriptomic analyses using next-generation sequencing have made it possible to determine the genomic region harboring the buckwheat S locus and to identify novel genes at this locus. In this review, we summarize the current knowledge on buckwheat heterostyly gained from conventional and molecular genetics and genomics. We also discuss the application of these studies to breeding of common buckwheat.

Genomics-assisted breeding in minor and pseudo-cereals

Minor and pseudo-cereals, which can grow with lower input and often produce specific nutrients compared to major cereal crops, are attracting worldwide attention. Since these crops generally have a large genetic diversity in a breeding population, rapid genetic improvement can be possible by the application of genomics-assisted breeding methods. In this review, we discuss studies related to biparental quantitative trait locus (QTL) mapping, genome-wide association study, and genomic selection for minor and pseudo-cereals. Especially, we focus on the current progress in a pseudo-cereal, buckwheat. Prospects for the practical utilization of genomics-assisted breeding in minor and pseudo-cereals are discussed including the issues to overcome especially for these crops.

The opposing effects of genetic drift and Haldane's sieve on floral-morph frequencies in tristylous metapopulations

Tristyly is a genetic floral polymorphism in which three floral morphs are maintained at equal frequencies by negative frequency-dependent selection on alleles at two interacting loci. Because dominant alleles at these loci are maintained at a lower frequency than their recessive counterparts, they are more likely to be lost by founder events and genetic drift. Here we examine the hypothesis that dominant alleles under negative frequency-dependent selection should also be more likely to re-invade populations than recessive alleles, due to Haldane's Sieve, because recessive alleles not expressed in a heterozygote state cannot benefit from positive selection when rare. We used computer simulations of tristylous metapopulations to verify that Haldane's Sieve acting on migrants into occupied demes can indeed reverse the bias in allele frequencies expected for small single tristylous populations, particularly in situations of rapid population growth following colonisation. This effect is manifest both locally and at the metapopulation level. Our study illustrates the potential effect of Haldane's Sieve in the novel context of an iconic plant sexual-system polymorphism under the influence of metapopulation dynamics.

The long and short of the S-locus in Turnera (Passifloraceae)

Distyly is an intriguing floral adaptation that increases pollen transfer precision and restricts inbreeding. It has been a model system in evolutionary biology since Darwin. Although the S-locus determines the long- and short-styled morphs, the genes were unknown in Turnera. We have now identified these genes. We used deletion mapping to identify, and then sequence, BAC clones and genome scaffolds to construct S/s haplotypes. We investigated candidate gene expression, hemizygosity, and used mutants, to explore gene function. The s-haplotype possessed 21 genes collinear with a region of chromosome 7 of grape. The S-haplotype possessed three additional genes and two inversions. TsSPH1 was expressed in filaments and anthers, TsYUC6 in anthers and TsBAHD in pistils. Long-homostyle mutants did not possess TsBAHD and a short-homostyle mutant did not express TsSPH1. Three hemizygous genes appear to determine S-morph characteristics in T. subulata. Hemizygosity is common to all distylous species investigated, yet the genes differ. The pistil candidate gene, TsBAHD, differs from that of Primula, but both may inactivate brassinosteroids causing short styles. TsYUC6 is involved in auxin synthesis and likely determines pollen characteristics. TsSPH1 is likely involved in filament elongation. We propose an incompatibility mechanism involving TsYUC6 and TsBAHD.

'A most complex marriage arrangement': recent advances on heterostyly and unresolved questions

Heterostylous genetic polymorphisms provide paradigmatic systems for investigating adaptation and natural selection. Populations are usually comprised of two (distyly) or three (tristyly) mating types, maintained by negative frequency-dependent selection resulting from disassortative mating. Theory predicts this mating system should result in equal style-morph ratios (isoplethy) at equilibrium. Here, I review recent advances on heterostyly, focusing on examples challenging stereotypical depictions of the polymorphism and unresolved questions. Comparative analyses indicate multiple origins of heterostyly, often within lineages. Ecological studies demonstrate that structural components of heterostyly are adaptations improving the proficiency of animal-mediated cross-pollination and reducing pollen wastage. Both neutral and selective processes cause deviations from isoplethy in heterostylous populations, and, under some ecological and demographic conditions, cause breakdown of the polymorphism, resulting in either the evolution of autogamy and mixed mating, or transitions to alternative outcrossing systems, including dioecy. Earlier ideas on the genetic architecture of the S-locus supergene governing distyly have recently been overturned by discovery that the dominant S-haplotype is a hemizygous region absent from the s-haplotype. Ecological, phylogenetic and molecular genetic data have validated some features of theoretical models on the selection of the polymorphism. Although heterostyly is the best-understood floral polymorphism in angiosperms, many unanswered questions remain.

Phylogenomic analysis reveals multiple evolutionary origins of selfing from outcrossing in a lineage of heterostylous plants

Evolutionary transitions from outcrossing to selfing often occur in heterostylous plants. Selfing homostyles originate within distylous populations and frequently evolve to become reproductively isolated species. We investigated this process in 10 species of Primula section Obconicolisteri using phylogenomic approaches and inferred how often homostyly originated from distyly and its consequences for population genetic diversity and floral trait evolution. We estimated phylogenetic relationships and reconstructed character evolution using the whole plastome comprised of 76 protein-coding genes. To investigate mating patterns and genetic diversity we screened 15 microsatellite loci in 40 populations. We compared floral traits among distylous and homostylous populations to determine how phenotypically differentiated homostyles were from their distylous ancestors. Section Obconicolisteri was monophyletic and we estimated multiple independent transitions from distyly to homostyly. High selfing rates characterised homostylous populations and this was associated with reduced genetic diversity. Flower size and pollen production were reduced in homostylous populations, but pollen size was significantly larger in some homostyles than in distylous morphs. Repeated transitions to selfing in section Obconicolisteri are likely to have been fostered by the complex montane environments that species occupy. Unsatisfactory pollinator service is likely to have promoted reproductive assurance in homostyles leading to subsequent population divergence through isolation.

Identification of a gene encoding polygalacturonase expressed specifically in short styles in distylous common buckwheat (Fagopyrum esculentum)

Common buckwheat (Fagopyrum esculentum) is a heteromorphic self-incompatible (SI) species with two types of floral architecture: thrum (short style) and pin (long style). The floral morphology and intra-morph incompatibility are controlled by a single genetic locus, S. However, the molecular mechanisms underlying the heteromorphic self-incompatibility of common buckwheat remain unclear. To identify these mechanisms, we performed proteomic, quantitative reverse-transcription PCR, and linkage analyses. Comparison of protein profiles between the long and short styles revealed a protein unique to the short style. Amino-acid sequencing revealed that it was a truncated form of polygalacturonase (PG); we designated the gene encoding this protein FePG1. Phylogenetic analysis classified FePG1 into the same clade as PGs that function in pollen development and floral morphology. FePG1 expression was significantly higher in short styles than in long styles. It was expressed in flowers of a short-homostyle line but not in flowers of a long-homostyle line. Linkage analysis indicated that FePG1 was not linked to the S locus; it could be a factor downstream of this locus. Our finding of a gene putatively working under the regulation of the S locus provides useful information for elucidation of the mechanism of heteromorphic self-incompatibility.

Global transcriptome and gene co-expression network analyses on the development of distyly in Primula oreodoxa

Distyly is a genetically controlled flower polymorphism that has intrigued both botanists and evolutionary biologists ever since Darwin's time. Despite extensive reports on the pollination and evolution of distylous systems, the genetic basis and mechanism of molecular regulation remain unclear. In the present study, comparative transcriptome profiling was conducted in primrose (Primula oreodoxa), the prime research model for heterostyly. Thirty-six transcriptomes were sequenced for styles at different stages and corolla tube in the three morphs of P. oreodoxa. Large numbers of differentially expressed genes (DEGs) were detected in the transcriptomes of styles across different morphs. Several transcription factors (TFs) and phytohormone metabolism-related genes were highlighted in S-morphs. A growing number of genes showed differential expression patterns along with the development of styles, suggesting that the genetic control of distyly may be more complicated than ever expected. Analysis of co-expression networks and module-trait relationships identified modules significantly associated with style development. CYP734A50, a key S-locus gene whose products degrade brassinosteroids, was co-expressed with many genes in the module and showed significant negative association with style length. In addition, crucial TFs involved in phytohormone signaling pathways were found to be connected with CYP734A50 in the co-expression module. Our global transcriptomic analysis has identified DEGs that are potentially involved in regulation of style length in P. oreodoxa, and may shed light on the evolution and broad biological processes of heterostyly.

Intraspecific variation of self-incompatibility in the distylous plant Primula merrilliana

Heteromorphic self-incompatibility can prevent self- and intramorph fertilization while favouring intermorph mating and the maintenance of morph-ratio stability in heterostylous populations. However, variation in the expression of self-incompatibility intraspecies has seldom been assessed. Through hand pollinations and microsatellite markers, the variation in the expression of self-incompatibility and genetic diversity were studied in distylous plant Primula merrilliana. We discovered that the strength of self-incompatibility varied extensively among individuals and populations, from pronounced to weaker self-incompatibility in distylous populations, all the way to strong self-compatibility in homostylous populations. Each distylous population included self-incompatible (SI), partly self-compatible (PSC) and self-compatible (SC) individuals, with the index of self-compatibility (ISC) ranging from 0.07 to 0.68 across populations. Self-compatible populations (ISC > 0.25) were not genetically clustered but were more closely related to populations with high SI and SC individuals were mixed with SI individuals within populations. The ISC and the proportions of SC and PSC individuals were higher in peripheral than in central populations, but no decrease of genetic diversity and no deviations of floral morph ratio from isoplethy were detected in peripheral populations. Additionally, the expression of self-incompatibility was stronger in long-styled flowers than in short-styled flowers. The variation in the strength of self-incompatibility documented in P. merrilliana cautions against the estimation of ISC from a few individuals or populations in distylous species and provides a more complex and nuanced understanding of the role of self-incompatibility in heterostyly.

Architectural constraints, male fertility variation and biased floral morph ratios in tristylous populations

Tristyly is a genetic polymorphism in which populations are comprised of three floral morphs (mating types) differing reciprocally in sex-organ height. Intermorph (disassortative) mating governed by a trimorphic incompatibility system should result in 1:1:1 morph ratios at equilibrium, but both deterministic and stochastic processes can cause skewed morph ratios in tristylous populations. Here, we investigate mechanisms causing morph-ratio bias in Pontederia parviflora, an emergent aquatic native to tropical America. We compared reproductive traits among morphs and surveyed 71 populations to determine patterns of morph-ratio bias. We then used simulation models of morph-frequency dynamics to test the hypothesis that morph-specific differences in pollen production and their influence on male fertility can explain patterns of morph-ratio bias. Ninety-seven percent of populations that we sampled were tristylous, but with a significant excess of the short-styled morph and a deficiency of the long-styled morph. Atypically for a tristylous species, mid-level anthers of the short-styled morph produced over twice as much pollen compared with the corresponding anthers of the long-styled morph. Our computer models incorporating this difference in male fertility resulted in morph ratios not significantly different from the average frequencies from our survey suggesting that the short-styled morph is more successful than the long-styled morph in siring ovules of the mid-styled morph. We propose that the difference in male fertility between morphs may be a non-adaptive consequence of a developmental constraint caused by the architecture of tristyly in Pontederiaceae.

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene

Primula vulgaris (primrose) exhibits heterostyly: plants produce self-incompatible pin- or thrum-form flowers, with anthers and stigma at reciprocal heights. Darwin concluded that this arrangement promotes insect-mediated cross-pollination; later studies revealed control by a cluster of genes, or supergene, known as the S (Style length) locus. The P. vulgaris S locus is absent from pin plants and hemizygous in thrum plants (thrum-specific); mutation of S locus genes produces self-fertile homostyle flowers with anthers and stigma at equal heights. Here, we present a 411 Mb P. vulgaris genome assembly of a homozygous inbred long homostyle, representing ~87% of the genome. We annotate over 24,000 P. vulgaris genes, and reveal more genes up-regulated in thrum than pin flowers. We show reduced genomic read coverage across the S locus in other Primula species, including P. veris, where we define the conserved structure and expression of the S locus genes in thrum. Further analysis reveals the S locus has elevated repeat content (64%) compared to the wider genome (37%). Our studies suggest conservation of S locus genetic architecture in Primula, and provide a platform for identification and evolutionary analysis of the S locus and downstream targets that regulate heterostyly in diverse heterostylous species.

Genetics of distyly and homostyly in a self-compatible Primula

The transition from outcrossing to selfing through the breakdown of distyly to homostyly has occurred repeatedly among families of flowering plants. Homostyles can originate by major gene changes at the S-locus linkage group, or by unlinked polygenic modifiers. Here, we investigate the inheritance of distyly and homostyly in Primula oreodoxa, a subalpine herb endemic to Sichuan, China. Controlled self- and cross-pollinations confirmed that P. oreodoxa unlike most heterostylous species is fully self-compatible. Segregation patterns indicated that the inheritance of distyly is governed by a single Mendelian locus with the short-styled morph carrying at least one dominant S-allele (S-) and long-styled plants homozygous recessive (ss). Crossing data were consistent with a model in which homostyly results from genetic changes at the distylous linkage group, with the homostylous allele (S^h) dominant to the long-styled allele (s), but recessive to the short-styled allele (S). Progeny tests of open-pollinated seed families revealed high rates of intermorph mating in the L-morph but considerable selfing and possibly intramorph mating in the S-morph and in homostyles. S-morph plants homozygous at the S-locus (SS) occurred in several populations but may experience viability selection. The crossing data from distylous and homostylous plants are consistent with either recombination at the S-locus governing distyly, or mutation at gene(s) controlling sex-organ height; both models predict the same patterns of segregation. Recent studies on the molecular genetics of distyly in Primula demonstrating the hemizygous nature of genes at the S-locus make it more likely that homostyles have resulted from mutation rather than recombination.

Potential of Genomic Selection in Mass Selection Breeding of an Allogamous Crop: An Empirical Study to Increase Yield of Common Buckwheat

To evaluate the potential of genomic selection (GS), a selection experiment with GS and phenotypic selection (PS) was performed in an allogamous crop, common buckwheat (Fagopyrum esculentum Moench). To indirectly select for seed yield per unit area, which cannot be measured on a single-plant basis, a selection index was constructed from seven agro-morphological traits measurable on a single plant basis. Over 3 years, we performed two GS and one PS cycles per year for improvement in the selection index. In GS, a prediction model was updated every year on the basis of genotypes of 14,598-50,000 markers and phenotypes. Plants grown from seeds derived from a series of generations of GS and PS populations were evaluated for the traits in the selection index and other yield-related traits. GS resulted in a 20.9% increase and PS in a 15.0% increase in the selection index in comparison with the initial population. Although the level of linkage disequilibrium in the breeding population was low, the target trait was improved with GS. Traits with higher weights in the selection index were improved more than those with lower weights, especially when prediction accuracy was high. No trait changed in an unintended direction in either GS or PS. The accuracy of genomic prediction models built in the first cycle decreased in the later cycles because the genetic bottleneck through the selection cycles changed linkage disequilibrium patterns in the breeding population. The present study emphasizes the importance of updating models in GS and demonstrates the potential of GS in mass selection of allogamous crop species, and provided a pilot example of successful application of GS to plant breeding.

Style polymorphism in Linum (Linaceae): a case of Mediterranean parallel evolution?

Heterostyly is a sex polymorphism that has challenged evolutionary biologists ever since Darwin. One of the lineages where heterostyly and related stylar conditions appear more frequently is Linum (Linaceae). This group is particularly suitable for testing competing hypotheses about ancestral and transitional stages on the evolutionary building up of heterostyly. We generated a phylogeny of Linum based on extensive sampling and plastid and nuclear DNA sequences, and used it to trace the evolution of character states of style polymorphism. We also revised available data on pollination, breeding systems, and polyploidy to analyse their associations. Our results supported former phylogenetic hypotheses: the paraphyly of Linum and the non-monophyly of current taxonomic sections. Heterostyly was common in the genus, but appeared concentrated in the Mediterranean Basin and the South African Cape. Ancestral character state reconstruction failed to determine a unique state as the most probable condition for style polymorphism in the genus. In contrast, approach herkogamy was resolved as ancestral state in some clades, giving support to recent hypotheses. Some traits putatively related to heterostyly, such as life history and polyploidy, did show marginal or non-significant phylogenetic correlation, respectively. Although pollinator data are limited, we suggest that beeflies are associated with specific cases of heterostyly. The consistent association between style polymorphism and heteromorphic incompatibility points to ecological factors as drivers of the multiple evolution of style polymorphism in Linum. Albeit based on limited evidence, we hypothesised that specialised pollinators and lack of mating opportunities drive evolution of style polymorphism and loss of the polymorphism, respectively.

Pollen and stigma size changes during the transition from tristyly to distyly in Oxalis alpina (Oxalidaceae)

Pollen and stigma size have the potential to influence male fitness of hermaphroditic plants, particularly in species presenting floral polymorphisms characterised by marked differences in these traits among floral morphs. In this study, we take advantage of the evolutionary transition from tristyly to distyly experienced by Oxalis alpina (Oxalidaceae), and examined whether modifications in the ancillary traits (pollen and stigma size) respond to allometric changes in other floral traits. Also, we tested whether these modifications are in accordance with what would be expected under the hypothesis that novel competitive scenarios (as in distylous-derived reproductive system) exert morph- and whorl-specific selective pressures to match the available stigmas. We measure pollen and stigma size in five populations of O. alpina representing the tristyly-distyly transition. A general reduction in pollen and stigma size occurred along the tristyly-distyly transition, and pollen size from the two anther levels within each morph converged to a similar size that was characterised by whorl-specific changes (increases or decreases) in pollen size of different anthers in each floral type. Overall, results from this study show that the evolution of distyly in this species is characterised not only by changes in sexual organ position and flower size, but also by morph-specific changes in pollen and stigma size. This evidence supports the importance of selection on pollen and stigma size, which increase fitness of remaining morphs following the evolution of distyly, and raises questions to explore on the functional value of pollen size in heterostylous systems under pollen competition.

Phylogeographic insights on the evolutionary breakdown of heterostyly

The breakdown of heterostyly to homostyly is a classic system for the investigation of evolutionary transitions from outcrossing to selfing. Loss of sexual polymorphism is characterized by changes to population morph structure and floral morphology. Here, we used molecular phylogeography to investigate the geographical context for the breakdown process in Primula chungensis, a species with distylous and homostylous populations. We genotyped plants from 20 populations throughout the entire range in south-west China using the chloroplast intergenic spacer (trnL-trnF), nuclear internal transcribed spacer (ITS) and 10 nuclear microsatellite loci, and determined the genetic relationships among populations and the variation in floral traits associated with homostyle evolution. The marker data identified two multi-population lineages (Tibet and Sichuan) and one single-population lineage (Yunnan), a pattern consistent with at least two independent origins of homostyly. Evidence from flower and pollen size variation is consistent with the hypothesis that transitions to selfing have arisen by the same genetic mechanism involving recombination and/or mutation at the distyly linkage group. Nevertheless, flowers of homostylous lineages have followed divergent evolutionary trajectories following their origin, resulting in populations with both approach and reverse herkogamy. Our study illustrates a rare example of the near-complete replacement of sexual polymorphism by floral monomorphism in a heterostylous species.

Genetic architecture and balancing selection: the life and death of differentiated variants

Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.

Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses

Heterostyly is a wide-spread floral adaptation to promote outbreeding, yet its genetic basis and evolutionary origin remain poorly understood. In Primula (primroses), heterostyly is controlled by the S-locus supergene that determines the reciprocal arrangement of reproductive organs and incompatibility between the two morphs. However, the identities of the component genes remain unknown. Here, we identify the Primula CYP734A50 gene, encoding a putative brassinosteroid-degrading enzyme, as the G locus that determines the style-length dimorphism. CYP734A50 is only present on the short-styled S-morph haplotype, it is specifically expressed in S-morph styles, and its loss or inactivation leads to long styles. The gene arose by a duplication specific to the Primulaceae lineage and shows an accelerated rate of molecular evolution. Thus, our results provide a mechanistic explanation for the Primula style-length dimorphism and begin to shed light on the evolution of the S-locus as a prime model for a complex plant supergene.

DOI:http://dx.doi.org/10.7554/eLife.17956.001

Flowers are highly specialized structures that many plants use to reproduce. Male organs called stamens on the flowers make pollen that can be transferred – usually by insect carriers or the wind – to a female structure called the stigma on another plant. However, since many flowers contain both male and female organs, it is also possible for the pollen to land on the stigma of the same flower, leading to a process called “self-fertilization”.

Many plants have developed mechanisms that prevent self-fertilization. For example, primroses produce two different types of flowers that arrange their stamens and stigmas differently. The stigma sits on the top of a stalk known as the style. Some primroses produce flowers with short stamens and a long style, resulting in the stigma being located high up in the flower (“pin” flowers), while others produce flowers with a short style and long stamens (“thrum” flowers). Primrose pollen is carried by insects and the different lengths of the styles and stamens make it more likely that pollen from a pin flower will land on the stigma of a thrum flower instead of a pin flower (and vice versa).

Although primrose flowers have fascinated botanists for centuries, the genes responsible for making the two types of flower had not been identified. Genetic studies indicated that different genes control the length of the stamens and style. However, these genes appear to be very close to each other on primrose DNA, which made it difficult to study them individually.

Huu et al. identified a gene called CYP734A50 that is responsible for the difference in style length in the flowers of a primrose called Primula veris. The gene is only present in the plants that have thrum flowers across a wide range of primrose species and genetic mutations that inactivate the gene in these plants result in flowers with longer styles. CYP734A50 encodes an enzyme that breaks down plant hormones called brassinosteroids, which normally promote growth. Treating thrum flowers with brassinosteroids increased the length of the styles. Future challenges are to identify the other genes that are responsible for producing pin and thrum flowers and to understand how this group of genes evolved.

DOI:http://dx.doi.org/10.7554/eLife.17956.002

Both morph- and species-dependent asymmetries affect reproductive barriers between heterostylous species

The interaction between floral traits and reproductive isolation is crucial to explaining the extraordinary diversity of angiosperms. Heterostyly, a complex floral polymorphism that optimizes outcrossing, evolved repeatedly and has been shown to accelerate diversification in primroses, yet its potential influence on isolating mechanisms remains unexplored. Furthermore, the relative contribution of pre- versus postmating barriers to reproductive isolation is still debated. No experimental study has yet evaluated the possible effects of heterostyly on pre- and postmating reproductive mechanisms. We quantify multiple reproductive barriers between the heterostylous Primula elatior (oxlip) and P. vulgaris (primrose), which readily hybridize when co-occurring, and test whether traits of heterostyly contribute to reproductive barriers in unique ways. We find that premating isolation is key for both species, while postmating isolation is considerable only for P. vulgaris; ecogeographic isolation is crucial for both species, while phenological, seed developmental, and hybrid sterility barriers are also important in P. vulgaris, implicating sympatrically higher gene flow into P. elatior. We document for the first time that, in addition to the aforementioned species-dependent asymmetries, morph-dependent asymmetries affect reproductive barriers between heterostylous species. Indeed, the interspecific decrease of reciprocity between high sexual organs of complementary floral morphs limits interspecific pollen transfer from anthers of short-styled flowers to stigmas of long-styled flowers, while higher reciprocity between low sexual organs favors introgression over isolation from anthers of long-styled flowers to stigmas of short-styled flowers. Finally, intramorph incompatibility persists across species boundaries, but is weakened in long-styled flowers of P. elatior, opening a possible backdoor to gene flow through intramorph pollen transfer between species. Therefore, patterns of gene flow across species boundaries are likely affected by floral morph composition of adjacent populations. To summarize, our study highlights the general importance of premating isolation and newly illustrates that both morph- and species-dependent asymmetries shape boundaries between heterostylous species.

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.

Variation in style morph frequencies in tristylous Lythrum salicaria in the Iberian Peninsula: the role of geographical and demographic factors

BACKGROUND AND AIMS

The balance between stochastic forces and negative frequency-dependent selection largely determines style morph frequencies in heterostylous populations. Investigation of morph frequencies at geographical range limits can provide insights into the forces maintaining the floral polymorphism, and the factors causing biased morph ratios. Here, we investigate style morph frequencies in populations at the south-western European range limit of tristylous Lythrum salicaria, to explore the role of demographic and geographical factors influencing morph ratios in its native range.

METHODS

We measured morph composition and evenness, and the size of 96 populations, along a north to south latitudinal transect from Galicia to Andalucia, Iberian Peninsula, traversing a steep climatic gradient. To examine the potential influence of morph-specific fitness components on morph ratios, we examined reproductive traits in 19 populations.

KEY RESULTS

Most populations of L. salicaria were trimorphic (94·79 %), the majority exhibiting 1 : 1 : 1 morph ratios (68·75 %). Populations with biased morph ratios had a deficiency of the short-styled morph. Population size and morph evenness were positively associated with latitude, with smaller populations and those with less even morph ratios occurring towards the south. Greater variance in morph evenness was evident at the southern range margin. There were no consistent differences in components of reproductive fitness among style morphs, but southern populations produced less fruit and seed than more northerly populations.

CONCLUSIONS

Our results demonstrate the influence of finite population size on morph frequencies in L. salicaria. However, they also illustrate the resilience of Iberian populations to the factors causing deviations from isoplethy and morph loss, especially at the southern range limit where populations are smaller. The maintenance of tristyly in small populations of L. salicaria may be aided by the genetic connectivity of populations in agricultural landscapes resulting from gene flow through pollen and seed dispersal.

On the origins of observations of heterostyly in Primula

In 1862, Charles Darwin published his landmark study on the different forms of flower in Primula; he coined the term distyly and subsequently expanded his studies to other species, including those with tristyly. Darwin is widely recognized as the first to study pin and thrum flowers in Primula, and to provide an explanation for the functional significance of the two floral morphs. Our laboratory is pursuing the genes that underpin floral heteromorphy in Primula, work influenced by Darwin's observations. One day, while appreciating a print of Primula vulgaris from William Curtis' Flora Londinensis, I was struck by the fact that I was looking at images of dimorphic Primula flowers captured in a late-1700s copper-plate engraving that predated Darwin's observations by over 70 yr. This realization triggered a journey into archives of botanical texts, herbals and florilegia from the 16(th) to 19(th) Centuries, and correspondence archives, in search of earlier documents that could have influenced Darwin and the origins of an idea. Darwin was not the first to observe floral heteromorphy in Primula, but he was the first to realize the significance of the two floral morphs. Darwin's insight and exposition of purpose have underpinned all consequent work on the subject.

Is heterostyly rare on oceanic islands?

Heterostyly has been considered rare or absent on oceanic islands. However, there has been no comprehensive review on this issue. Is heterostyly truly rare on oceanic islands? What makes heterostyly rare on such islands? To answer these questions, we review the reproductive studies on heterostyly on oceanic islands, with special emphasis on the heterostylous genus Psychotria in the Pacific Ocean as a model system. Overall, not many reproductive studies have been performed on heterostylous species on oceanic islands. In Hawaiian Psychotria, all 11 species are thought to have evolved dioecy from distyly. In the West Pacific, three species on the oceanic Bonin and Lanyu Islands are distylous (Psychotria homalosperma, P. boninensis and P. cephalophora), whereas three species on the continental Ryukyu Islands show various breeding systems, such as distyly (P. serpens), dioecy (P. rubra) and monoecy (P. manillensis). On some other Pacific oceanic islands, possibilities of monomorphy have been reported. For many Psychotria species, breeding systems are unknown, although recent studies indicate that heterostylous species may occur on some oceanic islands. A shift from heterostyly to other sexual systems may occur on some oceanic islands. This tendency may also contribute to the rarity of heterostyly, in addition to the difficulty in colonization/autochthonous evolution of heterostylous species on oceanic islands. Further investigation of reproductive systems of Psychotria on oceanic islands using robust phylogenetic frameworks would provide new insights into plant reproduction on oceanic islands.

Range-wide population genetics and variation in morph ratio in style-dimorphic Narcissus papyraceus

•

PREMISE OF THE STUDY

Theoretical models state that natural selection and mating patterns account for floral morph ratio in style-polymorphic plants. However, the demographic history of populations can also influence variation in morph ratios. If so, we hypothesize an association between the morph ratios and the genetic structure across populations.•

METHODS

We used nuclear microsatellites to assess genetic variation and structure in populations of Narcissus papyraceus, a style-dimorphic plant whose floral morph ratios (L-morph to S-morph) gradually vary throughout its distribution range in the southwestern Mediterranean Basin. We implemented analyses to relate the genetic features of populations with their morph ratios.•

KEY RESULTS

We found greater frequencies of the S-morph in central populations and declining frequencies toward the periphery. This geographic pattern was not associated with the genetic structure of populations. Instead, we found two distinct genetic groups, mainly separated by the Strait of Gibraltar, with a mixture of morph ratios within each one. Overall, there was a weak genetic structure. Genetic diversity was greater in central and southern dimorphic populations than in northern L-monomorphic populations.•

CONCLUSIONS

Altogether, our results do not support the hypothesis that the demographic history of populations can account for the observed geographical pattern of morph ratios in N. papyraceus. We suggest that adaptive processes shown in previous studies in the species are the main determinant of the existing variation in the morph composition of populations.

The draft genome of Primula veris yields insights into the molecular basis of heterostyly

Background

The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources.

Results

We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers.

Conclusions

The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0567-z) contains supplementary material, which is available to authorized users.

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.